Title: Microbial Pan-Genome Analysis
Description: A collection of functions for computations and visualizations of
microbial pan-genomes.
Author: Lars Snipen and Kristian Hovde Liland
Maintainer: Lars Snipen <lars.snipen@nmbu.no>
Diff between micropan versions 1.0 dated 2014-09-09 and 1.1 dated 2016-12-06
micropan-1.0/micropan/R/biostrings.R |only micropan-1.0/micropan/R/eclust.R |only micropan-1.0/micropan/R/fasta.R |only micropan-1.0/micropan/R/utilityfun.R |only micropan-1.0/micropan/data/Mpneumoniae.blast.clustering.RData |only micropan-1.0/micropan/data/Mpneumoniae.blast.distances.RData |only micropan-1.0/micropan/data/Mpneumoniae.blast.panmat.RData |only micropan-1.0/micropan/data/Mpneumoniae.domain.clustering.RData |only micropan-1.0/micropan/data/Mpneumoniae.domain.panmat.RData |only micropan-1.0/micropan/data/Mpneumoniae.table.RData |only micropan-1.0/micropan/man/binomixMachine.Rd |only micropan-1.0/micropan/man/gregexpr.Rd |only micropan-1.0/micropan/man/micropan-package.Rd |only micropan-1.0/micropan/man/negTruncLogLike.Rd |only micropan-1.0/micropan/man/plot.Binomix.Rd |only micropan-1.0/micropan/man/plot.Fasta.Rd |only micropan-1.0/micropan/man/plot.Panmat.Rd |only micropan-1.0/micropan/man/plot.Panpca.Rd |only micropan-1.0/micropan/man/plot.Pantree.Rd |only micropan-1.0/micropan/man/plot.Rarefac.Rd |only micropan-1.0/micropan/man/plotScores.Rd |only micropan-1.0/micropan/man/readFasta.Rd |only micropan-1.0/micropan/man/reverseComplement.Rd |only micropan-1.0/micropan/man/setLeafAttributes.Rd |only micropan-1.0/micropan/man/translate.Rd |only micropan-1.1/micropan/DESCRIPTION | 16 micropan-1.1/micropan/MD5 | 129 +-- micropan-1.1/micropan/NAMESPACE | 71 ++ micropan-1.1/micropan/R/bclust.R |only micropan-1.1/micropan/R/bdist.R | 338 +++++----- micropan-1.1/micropan/R/binomix.R | 228 +++++- micropan-1.1/micropan/R/blasting.R | 123 +++ micropan-1.1/micropan/R/domainclust.R | 220 ++++-- micropan-1.1/micropan/R/entrez.R | 169 +++-- micropan-1.1/micropan/R/genomedistances.R | 182 +++++ micropan-1.1/micropan/R/hmmer3.R | 111 +++ micropan-1.1/micropan/R/mpneumoniae.R |only micropan-1.1/micropan/R/panmat.R | 101 ++ micropan-1.1/micropan/R/panpca.R | 232 ++++++ micropan-1.1/micropan/R/panprep.R | 66 + micropan-1.1/micropan/R/powerlaw.R | 103 ++- micropan-1.1/micropan/R/prodigal.R | 84 +- micropan-1.1/micropan/R/rarefaction.R | 155 +++- micropan-1.1/micropan/R/trees.R | 139 +++- micropan-1.1/micropan/R/xz.R | 38 + micropan-1.1/micropan/build/vignette.rds |binary micropan-1.1/micropan/data/Mpneumoniae.blast.clustering.rda |only micropan-1.1/micropan/data/Mpneumoniae.blast.distances.rda |only micropan-1.1/micropan/data/Mpneumoniae.blast.panmat.rda |only micropan-1.1/micropan/data/Mpneumoniae.domain.clustering.rda |only micropan-1.1/micropan/data/Mpneumoniae.domain.panmat.rda |only micropan-1.1/micropan/data/Mpneumoniae.table.rda |only micropan-1.1/micropan/inst/doc/casestudy.pdf |binary micropan-1.1/micropan/man/bClust.Rd | 84 +- micropan-1.1/micropan/man/bDist.Rd | 98 +- micropan-1.1/micropan/man/binomixEstimate.Rd | 133 ++- micropan-1.1/micropan/man/blastAllAll.Rd | 138 ++-- micropan-1.1/micropan/man/chao.Rd | 55 - micropan-1.1/micropan/man/dClust.Rd | 75 +- micropan-1.1/micropan/man/distJaccard.Rd | 53 - micropan-1.1/micropan/man/distManhattan.Rd | 73 +- micropan-1.1/micropan/man/entrezDownload.Rd | 95 +- micropan-1.1/micropan/man/fluidity.Rd | 61 + micropan-1.1/micropan/man/geneWeights.Rd | 60 + micropan-1.1/micropan/man/generic.Binomix.Rd |only micropan-1.1/micropan/man/generic.Panmat.Rd |only micropan-1.1/micropan/man/generic.Panpca.Rd |only micropan-1.1/micropan/man/generic.Pantree.Rd |only micropan-1.1/micropan/man/generic.Rarefac.Rd |only micropan-1.1/micropan/man/getAccessions.Rd | 75 +- micropan-1.1/micropan/man/heaps.Rd | 74 +- micropan-1.1/micropan/man/hmmerCleanOverlap.Rd | 75 +- micropan-1.1/micropan/man/hmmerScan.Rd | 120 ++- micropan-1.1/micropan/man/isOrtholog.Rd | 81 +- micropan-1.1/micropan/man/mpneumoniae.Rd | 67 + micropan-1.1/micropan/man/panMatrix.Rd | 60 + micropan-1.1/micropan/man/panPrep.Rd | 76 +- micropan-1.1/micropan/man/panTree.Rd | 98 +- micropan-1.1/micropan/man/panpca.Rd | 107 ++- micropan-1.1/micropan/man/prodigalPredict.Rd | 76 +- micropan-1.1/micropan/man/rarefaction.Rd | 57 + micropan-1.1/micropan/man/readBlastTable.Rd | 40 - micropan-1.1/micropan/man/readHmmer.Rd | 53 - micropan-1.1/micropan/man/scores.loadings.Rd |only micropan-1.1/micropan/man/xz.Rd | 90 +- 85 files changed, 3233 insertions(+), 1346 deletions(-)
Title: Linked Micromap Plots for General U. S. Geographic Areas
Description: Provides the users with the ability to quickly create Linked
Micromap plots for a collection of geographic areas.
Linked Micromaps are visualizations of georeferenced data that link statistical
graphics to an organized series of small maps or graphic images.
The Help description contains examples of how to use the micromapST function.
Contained in this package are border group datasets to support creating micromaps for the
50 U.S. states and District of Columbia (51 areas), the U. S. 20 Seer Registries,
the 105 counties in the state of Kansas, the 62 counties of New York,
the 24 counties of Maryland, the 29 counties of Utah, the 32 administrative areas
in China, the 218 administrative areas in the UK and Ireland (for testing only),
the 25 districts in the city of Seoul South Korea, and the 52 counties on the Africa
continent.
A border group dataset contains the boundaries related to the data level areas,
a second layer boundaries, a top or third layer boundary, a parameter list of
run options, and a cross indexing table between area names, abbreviations,
numeric identification and alias matching strings for the specific geographic
area. By specifying a border group, the package create micromaps for any
geographic region. The user can create and provide their own border group dataset
for any area beyond the areas contained within the package.
Copyrighted 2013, 2014, 2015 and 2016 by Carr, Pearson and Pickle.
Author: Jim Pearson <jpearson@statnetconsulting.com> and Dan Carr <dcarr@gmu.edu>,
with contributions from Linda Pickle <linda@statnetconsulting.com>.
Maintainer: Jim Pearson <jpearson@statnetconsulting.com>
Diff between micromapST versions 1.0.5 dated 2015-01-21 and 1.1.0 dated 2016-12-06
micromapST-1.0.5/micromapST/NEWS |only micromapST-1.0.5/micromapST/data/Educ8thData.RData |only micromapST-1.0.5/micromapST/data/TSdata.RData |only micromapST-1.0.5/micromapST/data/segBarData.rda |only micromapST-1.0.5/micromapST/data/stateNamesFips.rda |only micromapST-1.0.5/micromapST/data/stateNationVisBorders.rda |only micromapST-1.0.5/micromapST/data/stateVisBorders.rda |only micromapST-1.0.5/micromapST/man/micromapSTDefaults.Rd |only micromapST-1.0.5/micromapST/man/micromapSTSetDefaults.Rd |only micromapST-1.0.5/micromapST/man/segBarData.Rd |only micromapST-1.0.5/micromapST/man/stateNamesFips.Rd |only micromapST-1.0.5/micromapST/man/stateNationVisBorders.Rd |only micromapST-1.0.5/micromapST/man/stateVisBorders.Rd |only micromapST-1.1.0/micromapST/DESCRIPTION | 49 micromapST-1.1.0/micromapST/MD5 | 112 micromapST-1.1.0/micromapST/NAMESPACE | 22 micromapST-1.1.0/micromapST/R/micromapDefSets.r |only micromapST-1.1.0/micromapST/R/micromapST.r |15905 ++++++++--- micromapST-1.1.0/micromapST/R/panelFunctions.r | 661 micromapST-1.1.0/micromapST/build/vignette.rds |binary micromapST-1.1.0/micromapST/data/AfricaBG.rda |only micromapST-1.1.0/micromapST/data/AfricaPopData.rda |only micromapST-1.1.0/micromapST/data/ChinaBG.rda |only micromapST-1.1.0/micromapST/data/Educ8thData.rda |only micromapST-1.1.0/micromapST/data/KansPopInc.rda |only micromapST-1.1.0/micromapST/data/KansasBG.rda |only micromapST-1.1.0/micromapST/data/MarylandBG.rda |only micromapST-1.1.0/micromapST/data/NewYorkBG.rda |only micromapST-1.1.0/micromapST/data/Seer18Area.rda |only micromapST-1.1.0/micromapST/data/SeoulPopData.rda |only micromapST-1.1.0/micromapST/data/SeoulSKoreaBG.rda |only micromapST-1.1.0/micromapST/data/TSdata.rda |only micromapST-1.1.0/micromapST/data/UKIrelandBG.rda |only micromapST-1.1.0/micromapST/data/UKIrelandPopData.rda |only micromapST-1.1.0/micromapST/data/UKIrelandPopData2.rda |only micromapST-1.1.0/micromapST/data/USSeerBG.rda |only micromapST-1.1.0/micromapST/data/USStatesBG.rda |only micromapST-1.1.0/micromapST/data/UtahBG.rda |only micromapST-1.1.0/micromapST/data/UtahPopData.rda |only micromapST-1.1.0/micromapST/data/cnPopData.rda |only micromapST-1.1.0/micromapST/data/detailsVariables.rda |only micromapST-1.1.0/micromapST/data/mdPopData.rda |only micromapST-1.1.0/micromapST/data/nyPopData.rda |only micromapST-1.1.0/micromapST/data/statePop2010.rda |binary micromapST-1.1.0/micromapST/data/wflung00and95.rda |binary micromapST-1.1.0/micromapST/data/wflung00and95US.rda |binary micromapST-1.1.0/micromapST/data/wflung00cnty.rda |binary micromapST-1.1.0/micromapST/data/wmlung5070.rda |binary micromapST-1.1.0/micromapST/data/wmlung5070US.rda |binary micromapST-1.1.0/micromapST/inst/CITATION | 51 micromapST-1.1.0/micromapST/inst/doc/JSSmicromapSTv63i03.pdf |binary micromapST-1.1.0/micromapST/inst/doc/NEWS |only micromapST-1.1.0/micromapST/man/AfricaBG.Rd |only micromapST-1.1.0/micromapST/man/AfricaPopData.Rd |only micromapST-1.1.0/micromapST/man/ChinaBG.Rd |only micromapST-1.1.0/micromapST/man/Educ8thData.Rd | 4 micromapST-1.1.0/micromapST/man/KansPopInc.Rd |only micromapST-1.1.0/micromapST/man/KansasBG.Rd |only micromapST-1.1.0/micromapST/man/MarylandBG.Rd |only micromapST-1.1.0/micromapST/man/NewYorkBG.Rd |only micromapST-1.1.0/micromapST/man/Seer18Area.Rd |only micromapST-1.1.0/micromapST/man/SeoulPopData.Rd |only micromapST-1.1.0/micromapST/man/SeoulSKoreaBG.Rd |only micromapST-1.1.0/micromapST/man/TSdata.Rd | 3 micromapST-1.1.0/micromapST/man/UKIrelandBG.Rd |only micromapST-1.1.0/micromapST/man/UKIrelandPopData.Rd |only micromapST-1.1.0/micromapST/man/USSeerBG.Rd |only micromapST-1.1.0/micromapST/man/USStatesBG.Rd |only micromapST-1.1.0/micromapST/man/UtahBG.Rd |only micromapST-1.1.0/micromapST/man/UtahPopData.Rd |only micromapST-1.1.0/micromapST/man/bordGrp.Rd |only micromapST-1.1.0/micromapST/man/cnPopData.Rd |only micromapST-1.1.0/micromapST/man/detailsVariables.Rd |only micromapST-1.1.0/micromapST/man/mdPopData.Rd |only micromapST-1.1.0/micromapST/man/messages.Rd |only micromapST-1.1.0/micromapST/man/micromapGDefaults.Rd |only micromapST-1.1.0/micromapST/man/micromapGSetDefaults.Rd |only micromapST-1.1.0/micromapST/man/micromapGSetPanelDef.Rd |only micromapST-1.1.0/micromapST/man/micromapSEER.Rd |only micromapST-1.1.0/micromapST/man/micromapST-package.Rd | 227 micromapST-1.1.0/micromapST/man/micromapST.Rd | 1037 micromapST-1.1.0/micromapST/man/nyPopData.Rd |only micromapST-1.1.0/micromapST/man/panelDesc.Rd | 405 micromapST-1.1.0/micromapST/man/statePop2010.Rd | 6 micromapST-1.1.0/micromapST/man/wflung00and95.Rd | 2 micromapST-1.1.0/micromapST/man/wflung00and95US.Rd | 2 micromapST-1.1.0/micromapST/man/wflung00cnty.Rd | 2 micromapST-1.1.0/micromapST/man/wmlung5070.Rd | 4 micromapST-1.1.0/micromapST/man/wmlung5070US.Rd | 2 89 files changed, 14291 insertions(+), 4203 deletions(-)
Title: ICES Vocabularies Database Web Services
Description: R interface to access the RECO POX web services of the ICES (International
Council for the Exploration of the Sea) Vocabularies database <http://vocab.ices.dk/services/POX.aspx>.
Author: Colin Millar [aut, cre],
Arni Magnusson [aut]
Maintainer: Colin Millar <colin.millar@ices.dk>
Diff between icesVocab versions 1.1-0 dated 2016-12-06 and 1.1-2 dated 2016-12-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 6 ++++++ R/utilities.R | 38 ++++++++++++++++++++++++++++---------- 4 files changed, 40 insertions(+), 16 deletions(-)
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>
Diff between btergm versions 1.7.6 dated 2016-06-18 and 1.8.1 dated 2016-12-06
DESCRIPTION | 14 - MD5 | 26 +-- NAMESPACE | 4 R/btergm.R | 202 ++++++++++++++++------- R/checkdegeneracy.R | 121 +++++++++----- R/gofmethods.R | 68 ++++---- R/gofstatistics.R | 2 R/interpretation.R | 257 +++++++++++++++--------------- R/mtergm.R | 58 ++++-- R/tergmprepare.R | 416 ++++++++++++++++++++++++------------------------- inst/CITATION | 10 - man/btergm-class.Rd | 9 - man/checkdegeneracy.Rd | 17 +- man/edgeprob.Rd | 13 - 14 files changed, 690 insertions(+), 527 deletions(-)
Title: Mark-Recapture Analysis for Survival and Abundance Estimation
Description: Functions for fitting various models to capture-recapture data
including fixed and mixed-effects Cormack-Jolly-Seber(CJS) for survival
estimation and POPAN structured Jolly-Seber models for abundance
estimation. Includes a CJS models that concurrently estimates and corrects
for tag loss. Hidden Markov model (HMM) implementations of CJS and
multistate models with and without state uncertainty.
Author: Jeff Laake <jeff.laake@noaa.gov>, Devin Johnson
<devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>
Maintainer: Jeff Laake <jefflaake@gmail.com>
Diff between marked versions 1.1.11 dated 2016-03-07 and 1.1.13 dated 2016-12-06
DESCRIPTION | 14 +- MD5 | 90 ++++++++------ NAMESPACE | 10 + NEWS | 54 ++++++++ R/HMMLikelihood.r | 85 +++++++++++-- R/HMMutilities.r | 4 R/InitialDistribution_functions.r | 13 +- R/Observation_functions.r | 2 R/RHMMLikelihood.r | 2 R/admbutils.R |only R/cjs.R | 50 -------- R/cjs_tmb.R |only R/create.dm.R | 97 ++++++++++----- R/create.dmdf.R | 3 R/crm.R | 233 +++++++++++++++++++++++++++----------- R/hsmm2hmm.r |only R/make.design.data.R | 65 ++++++++++ R/marked-package.R | 45 ++++++- R/mixed.model.r | 17 ++ R/mscjs.r | 184 +++++++++++++++++++----------- R/mvmscjs.R |only R/probitCJS.R | 10 - R/process.data.R | 3 R/scale.r | 7 - R/set.fixed.R | 5 R/setup.model.R | 8 + R/simplify.r | 26 ++++ build/vignette.rds |binary data/skagit.rda |only inst/cjs.tpl | 4 inst/cjs_tmb.cpp |only inst/cjsre_tmb.cpp |only inst/doc/markedVignette.pdf |binary inst/models.txt | 1 inst/multistate.tpl | 216 ++++++++++++++++++++++------------- inst/mvms.tpl |only inst/parameters.txt | 99 ++++++++-------- man/HMMLikelihood.Rd | 8 - man/cjs_delta.Rd | 1 man/cjs_tmb.Rd |only man/create.dmdf.Rd | 3 man/crm.Rd | 23 ++- man/dmat_hsmm2hmm.Rd |only man/hsmm2hmm.Rd |only man/initiate_pi.Rd |only man/mscjs.Rd | 89 +++++++++++++- man/mvmscjs.Rd |only man/sealions.Rd | 2 man/setup_admb.Rd |only man/setup_tmb.Rd |only man/skagit.Rd |only man/tagloss.Rd | 2 src/hmm_like.f | 4 src/mvmsdmat.f | 85 ++++++++----- 54 files changed, 1096 insertions(+), 468 deletions(-)
Title: Testset for Differential Equations
Description: Solvers and testset for stiff and nonstiff differential equations, and
differential algebraic equations.
Author: Karline Soetaert [aut, cre],
Jeff Cash [aut],
Francesca Mazzia [aut],
LAPACK authors [cph]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between deTestSet versions 1.1.2 dated 2014-12-03 and 1.1.3 dated 2016-12-06
DESCRIPTION | 15 ++-- MD5 | 65 ++++++++++--------- NAMESPACE | 4 + build/vignette.rds |binary inst/doc/examples/hires.R | 4 - man/deTestSet.Rd | 2 src/Ex_andrews.f | 2 src/Ex_beam.f | 34 ++++++---- src/Ex_car.f | 2 src/Ex_crank.f | 7 -- src/Ex_emep.f | 7 +- src/Ex_fekete.f | 2 src/Ex_hires.f | 8 +- src/Ex_pleiades.f | 6 - src/Ex_pollution.f | 8 +- src/Ex_ring.f | 2 src/Ex_transistor.f | 12 +-- src/Ex_tube.f | 2 src/Ex_twobit.f | 27 ++++---- src/Ex_wheelset.f | 2 src/bimd.f | 33 +++++++++- src/bimda.f | 150 +++++++++++++++++++++++++++++++++------------- src/call_dopri.c | 3 src/call_gam.c | 21 +++--- src/call_mebdfi.c | 13 ++- src/cashkarp.f | 62 ++++++++++++------- src/de_utils.c | 7 +- src/dopri6.f | 51 ++++++++++----- src/dopri8.f | 71 ++++++++++++++------- src/errmsg.f | 2 src/externalptr.h |only src/forcings.c | 6 + src/gamd.f90 | 50 +++++++++------ src/mebdfi.f | 40 ++++++++---- 34 files changed, 464 insertions(+), 256 deletions(-)
Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous or categorical data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2016; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means.
Author: Alfonso Iodice D'Enza [aut], Angelos Markos [aut, cre], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between clustrd versions 1.0.9 dated 2016-11-10 and 1.1.0 dated 2016-12-06
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/clu_means.R | 2 +- R/plot.clusmca.R | 28 ++++++++++++++-------------- R/tune_clusmca.R | 6 ++---- man/clusmca.Rd | 2 +- man/tune_clusmca.Rd | 8 ++++---- man/tune_cluspca.Rd | 4 ++-- 9 files changed, 38 insertions(+), 40 deletions(-)
Title: Estimation of the Relative Importance of Factors Affecting
Species Distribution Based on Stability Concept
Description: From output files obtained from the software 'ModestR', the relative contribution of factors to explain species distribution is depicted using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between SPEDInstabR versions 1.2 dated 2016-11-04 and 1.3 dated 2016-12-06
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- data/FishFC.RData |binary data/Instability.RData |binary data/VI.RData |binary data/adworld.RData |binary inst |only 7 files changed, 10 insertions(+), 9 deletions(-)
Title: Graphical User Interface for Package sdcMicro
Description: DEPRECATED: A new version of the graphical user interface is available
directly in the package sdcMicro via function sdcApp(). A point and click graphical
user interface based on top of the 'sdcMicro' package to create anonymized data set.
The graphical user interface provides full reproducibility of any result via the
script menu in the GUI.
Author: Alexander Kowarik, Matthias Templ, Bernhard Meindl, Francois Fonteneau
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between sdcMicroGUI versions 1.3.0 dated 2016-08-16 and 1.4.0 dated 2016-12-06
DESCRIPTION | 20 ++++++++++---------- MD5 | 10 +++++----- NEWS | 2 ++ R/sdcGUI.r | 3 +++ build/vignette.rds |binary inst/doc/gui_tutorial.pdf |binary 6 files changed, 20 insertions(+), 15 deletions(-)
Title: A Toolbox for the Analysis of Proteomics Data
Description: Tools for the statistical analysis and visualization of (relative
and absolute) quantitative (LFQ,TMT,HRM) Proteomics data.
Author: Erik Ahrne
Maintainer: Erik Ahrne <erik.ahrne@unibas.ch>
Diff between SafeQuant versions 2.3 dated 2016-10-04 and 2.3.1 dated 2016-12-06
SafeQuant-2.3.1/SafeQuant/DESCRIPTION | 10 +-- SafeQuant-2.3.1/SafeQuant/MD5 | 28 +++++----- SafeQuant-2.3.1/SafeQuant/NAMESPACE | 4 - SafeQuant-2.3.1/SafeQuant/R/Graphics.R | 20 +++++-- SafeQuant-2.3.1/SafeQuant/R/TMT.R | 4 - SafeQuant-2.3.1/SafeQuant/R/UserOptions.R | 4 - SafeQuant-2.3.1/SafeQuant/exec/safeQuant.R | 2 SafeQuant-2.3.1/SafeQuant/inst/manuals/SafeQuant-man.pdf |binary SafeQuant-2.3.1/SafeQuant/man/plotNbValidDeFeaturesPerFDR.Rd | 10 ++- SafeQuant-2.3.1/SafeQuant/tests/initTestSession.R | 6 -- SafeQuant-2.3.1/SafeQuant/tests/testData/SQ_Results |only SafeQuant-2.3.1/SafeQuant/tests/testData/skyline_transition_results.csv |only SafeQuant-2.3.1/SafeQuant/tests/testTMT.R | 2 SafeQuant-2.3/SafeQuant/R/Targeted.R |only SafeQuant-2.3/SafeQuant/man/calibrationCurve.Rd |only SafeQuant-2.3/SafeQuant/tests/testData/skyline_dilution_curve.csv |only SafeQuant-2.3/SafeQuant/tests/testTargeted.R |only 17 files changed, 48 insertions(+), 42 deletions(-)
Title: Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equations
Description: Routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of ordinary differential equations (ODE).
Includes routines that: (1) generate gradient and jacobian matrices (full and banded),
(2) find roots of non-linear equations by the 'Newton-Raphson' method,
(3) estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the 'Newton-Raphson' method, or by dynamically running,
(4) solve the steady-state conditions for uni-and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations
by numerical differencing (using the method-of-lines approach).
Includes fortran code.
Author: Karline Soetaert [aut, cre],
yale sparse matrix package authors [cph]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between rootSolve versions 1.6.6 dated 2015-10-05 and 1.7 dated 2016-12-06
DESCRIPTION | 18 MD5 | 61 R/Utilities.R | 6 R/runsteady.R | 124 +- R/steady.1D.R | 39 R/steady.2D.R | 28 R/steady.3D.R | 25 R/steady.R | 14 R/steady.band.R | 4 R/stode.R | 17 R/stodes.R | 21 build/vignette.rds |binary man/runsteady.Rd | 63 - man/steady.1D.Rd | 22 man/steady.2D.Rd | 29 man/steady.3D.Rd | 17 man/steady.Rd | 11 man/steady.band.Rd | 8 man/stode.Rd | 9 man/stodes.Rd | 7 src/call_runsteady.c | 33 src/call_steady.c | 7 src/call_stsparse.c | 3 src/dsparsk.f | 410 +++--- src/externalptr.h |only src/lsodes.f | 3153 +++++++++++++++++++++++++++++++++++++++++++++++++-- src/sparse.f | 158 +- src/sparsecoeff.f | 20 src/sparsekit.f | 2 src/steady.f | 4 src/steady_utils.c | 5 src/testMap.f | 12 32 files changed, 3816 insertions(+), 514 deletions(-)
Title: Solvers for Boundary Value Problems of Differential Equations
Description: Functions that solve boundary value problems ('BVP') of systems of ordinary
differential equations ('ODE') and differential algebraic equations ('DAE').
The functions provide an interface to the FORTRAN functions
'twpbvpC', 'colnew/colsys', and an R-implementation of the shooting method.
Author: Karline Soetaert <karline.soetaert@nioz.nl>,
Jeff Cash <j.cash@imperial.ac.uk>,
Francesca Mazzia <mazzia@dm.uniba.it>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between bvpSolve versions 1.3.2 dated 2015-09-22 and 1.3.3 dated 2016-12-06
DESCRIPTION | 10 MD5 | 41 +-- build/vignette.rds |binary inst/doc/bvpSolve.pdf |binary inst/doc/bvpTests.pdf |binary inst/doc/opuscula_math_3424.pdf |binary man/bvpSolve.Rd | 2 src/acdcR.f | 165 ++++++++---- src/bvpSolve_utils.c | 3 src/call_acdc.c | 9 src/call_colmodsys.c | 9 src/call_colnew.c | 15 - src/call_twpbvp.c | 11 src/coldaeR.f | 330 +++++++++++++++++-------- src/colmodR.f | 281 +++++++++++++++------ src/colnewR.f | 316 ++++++++++++++++-------- src/colsysR.f | 526 +++++++++++++++++++++++++++------------- src/externalptr.h |only src/forcings.c | 4 src/twpbvpa.f | 158 ++++++------ src/twpbvpc.f | 24 - src/twpbvplc.f | 47 +-- 22 files changed, 1309 insertions(+), 642 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial data, in R.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Michael Sumner [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.2-5 dated 2016-11-24 and 0.2-6 dated 2016-12-06
sf-0.2-5/sf/vignettes/rw.html |only sf-0.2-5/sf/vignettes/sfr.html |only sf-0.2-6/sf/DESCRIPTION | 10 sf-0.2-6/sf/MD5 | 92 +++--- sf-0.2-6/sf/NAMESPACE | 4 sf-0.2-6/sf/R/RcppExports.R | 24 + sf-0.2-6/sf/R/arith.R | 13 sf-0.2-6/sf/R/cast.R |only sf-0.2-6/sf/R/geom.R | 44 +-- sf-0.2-6/sf/R/grid.R | 2 sf-0.2-6/sf/R/read.R | 14 - sf-0.2-6/sf/R/sf.R | 1 sf-0.2-6/sf/R/sfc.R | 5 sf-0.2-6/sf/R/sp.R | 3 sf-0.2-6/sf/R/tidy.R | 2 sf-0.2-6/sf/build/vignette.rds |binary sf-0.2-6/sf/configure | 125 +++++++++ sf-0.2-6/sf/configure.in | 108 ++++++++ sf-0.2-6/sf/inst/doc/sf1.Rmd | 2 sf-0.2-6/sf/inst/doc/sf1.html | 18 - sf-0.2-6/sf/inst/doc/sf2.html | 10 sf-0.2-6/sf/inst/doc/sf3.R | 216 ++++++++++++++++ sf-0.2-6/sf/inst/doc/sf3.Rmd | 337 +++++++++++++++++++++++++ sf-0.2-6/sf/inst/doc/sf3.html | 447 +++++++++++++++++++++++++++++++++- sf-0.2-6/sf/man/dplyr.Rd | 2 sf-0.2-6/sf/man/geos.Rd | 2 sf-0.2-6/sf/man/st_cast.Rd |only sf-0.2-6/sf/man/st_read.Rd | 4 sf-0.2-6/sf/man/st_viewport.Rd | 2 sf-0.2-6/sf/man/st_write.Rd | 2 sf-0.2-6/sf/src/RcppExports.cpp | 74 +++-- sf-0.2-6/sf/src/gdal.cpp | 2 sf-0.2-6/sf/src/gdal_geom.cpp | 75 ----- sf-0.2-6/sf/src/geos.cpp | 128 +++++++++ sf-0.2-6/sf/src/wkb.cpp | 4 sf-0.2-6/sf/tests/Rplots.pdf |binary sf-0.2-6/sf/tests/dplyr.R | 2 sf-0.2-6/sf/tests/dplyr.Rout.save | 4 sf-0.2-6/sf/tests/gdal_geom.R | 2 sf-0.2-6/sf/tests/gdal_geom.Rout.save | 8 sf-0.2-6/sf/tests/geos.R | 4 sf-0.2-6/sf/tests/geos.Rout.save | 6 sf-0.2-6/sf/tests/grid.R | 6 sf-0.2-6/sf/tests/grid.Rout.save | 8 sf-0.2-6/sf/tests/sfc.R | 58 ++++ sf-0.2-6/sf/tests/sfc.Rout.save | 194 ++++++++++++++ sf-0.2-6/sf/tests/testthat/test_sfc.R | 2 sf-0.2-6/sf/vignettes/sf1.Rmd | 2 sf-0.2-6/sf/vignettes/sf3.Rmd | 337 +++++++++++++++++++++++++ 49 files changed, 2152 insertions(+), 253 deletions(-)
Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.rsp versions 0.30.0 dated 2016-05-15 and 0.40.0 dated 2016-12-06
R.rsp-0.30.0/R.rsp/R/DEPRECATED.compileRsp0.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.hexToInt.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.importRsp.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.parseRsp.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.rsp.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.rspCapture.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.rspToHtml.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.rsptex.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.sourceAllRsp.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.sourceRsp.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.sourceRspV2.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.translateRsp.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.translateRspV1.R |only R.rsp-0.30.0/R.rsp/R/DEPRECATED.urlDecode.R |only R.rsp-0.30.0/R.rsp/man/import.RspResponse.Rd |only R.rsp-0.30.0/R.rsp/man/importRsp.Rd |only R.rsp-0.30.0/R.rsp/man/parseRsp.Rd |only R.rsp-0.30.0/R.rsp/man/rsp.Rd |only R.rsp-0.30.0/R.rsp/man/rspToHtml.Rd |only R.rsp-0.30.0/R.rsp/man/rsptex.Rd |only R.rsp-0.30.0/R.rsp/man/sourceAllRsp.Rd |only R.rsp-0.30.0/R.rsp/man/sourceRsp.Rd |only R.rsp-0.30.0/R.rsp/man/translateRsp.Rd |only R.rsp-0.30.0/R.rsp/man/translateRspV1.Rd |only R.rsp-0.40.0/R.rsp/DESCRIPTION | 14 R.rsp-0.40.0/R.rsp/MD5 | 178 - R.rsp-0.40.0/R.rsp/NAMESPACE | 9 R.rsp-0.40.0/R.rsp/NEWS | 14 R.rsp-0.40.0/R.rsp/R/999.NonDocumentedObjects.R | 12 R.rsp-0.40.0/R.rsp/R/DEFUNCT.R |only R.rsp-0.40.0/R.rsp/R/HttpDaemon.processRsp.R | 23 R.rsp-0.40.0/R.rsp/R/RspDocument.R | 2 R.rsp-0.40.0/R.rsp/R/RspResponse.R | 43 R.rsp-0.40.0/R.rsp/R/findAsciiDoc.R | 26 R.rsp-0.40.0/R.rsp/R/findPandoc.R | 26 R.rsp-0.40.0/R.rsp/R/parseInternetMediaType.R | 2 R.rsp-0.40.0/R.rsp/R/rcat.R | 2 R.rsp-0.40.0/R.rsp/R/rclean.R | 2 R.rsp-0.40.0/R.rsp/R/rcode.R | 9 R.rsp-0.40.0/R.rsp/R/rcompile.R | 2 R.rsp-0.40.0/R.rsp/R/rfile.R | 2 R.rsp-0.40.0/R.rsp/R/rstring.R | 2 R.rsp-0.40.0/R.rsp/R/splitUrl.R | 2 R.rsp-0.40.0/R.rsp/R/xweavetangle.R | 28 R.rsp-0.40.0/R.rsp/build/vignette.rds |binary R.rsp-0.40.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.pdf |binary R.rsp-0.40.0/R.rsp/inst/doc/RSP_intro.html | 1625 +++++----- R.rsp-0.40.0/R.rsp/inst/doc/RSP_intro.md.rsp | 8 R.rsp-0.40.0/R.rsp/inst/doc/RSP_refcard.pdf |binary R.rsp-0.40.0/R.rsp/inst/doc/RSP_refcard.tex.rsp | 2 R.rsp-0.40.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.ltx | 9 R.rsp-0.40.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.pdf |binary R.rsp-0.40.0/R.rsp/inst/doc/R_packages-RSP_vignettes.html | 460 +- R.rsp-0.40.0/R.rsp/inst/doc/R_packages-RSP_vignettes.md.rsp | 2 R.rsp-0.40.0/R.rsp/inst/doc/R_packages-Static_PDF_and_HTML_vignettes.pdf |binary R.rsp-0.40.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.pdf |binary R.rsp-0.40.0/R.rsp/inst/rsp/R/help/index.html.rsp | 4 R.rsp-0.40.0/R.rsp/inst/rsp/R/settings/options.html.rsp | 4 R.rsp-0.40.0/R.rsp/inst/rsp/R/settings/par.html.rsp | 6 R.rsp-0.40.0/R.rsp/inst/rsp/R/system/environmentVariables.html.rsp | 2 R.rsp-0.40.0/R.rsp/inst/rsp/R/system/environments/index.html.rsp | 2 R.rsp-0.40.0/R.rsp/inst/rsp/R/system/ll.html.rsp | 4 R.rsp-0.40.0/R.rsp/inst/rsp/R/system/packages.html.rsp | 6 R.rsp-0.40.0/R.rsp/inst/rsp/R/system/systemDetails.html.rsp | 16 R.rsp-0.40.0/R.rsp/inst/rsp/index.html.rsp | 2 R.rsp-0.40.0/R.rsp/inst/rsp/rsp/demos/colors/index.html.rsp | 2 R.rsp-0.40.0/R.rsp/inst/rsp_examples/R_packages-Static_PDF_and_HTML_vignettes.tex.rsp | 3 R.rsp-0.40.0/R.rsp/inst/rsp_tests_online/latex,online.R | 2 R.rsp-0.40.0/R.rsp/man/FileRspResponse.Rd | 2 R.rsp-0.40.0/R.rsp/man/HttpDaemonRspResponse.Rd | 2 R.rsp-0.40.0/R.rsp/man/Non-documented_objects.Rd | 12 R.rsp-0.40.0/R.rsp/man/R.rsp-package.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspCode.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspCodeChunk.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspComment.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspConstruct.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspCutDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspDocument.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspErrorDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspEvalDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspIfDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspIncludeDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspMetaDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspPageDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspResponse.Rd | 1 R.rsp-0.40.0/R.rsp/man/RspUnknownDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspUnparsedDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/RspVariableDirective.Rd | 2 R.rsp-0.40.0/R.rsp/man/rargs.Rd | 2 R.rsp-0.40.0/R.rsp/man/rcode.Rd | 1 R.rsp-0.40.0/R.rsp/man/splitUrl.Rd | 2 R.rsp-0.40.0/R.rsp/tests/rargs.R |only R.rsp-0.40.0/R.rsp/tests/rcat.R | 4 R.rsp-0.40.0/R.rsp/tests/rcode.R | 3 R.rsp-0.40.0/R.rsp/tests/rcompile.R | 2 R.rsp-0.40.0/R.rsp/tests/rfile.R | 2 R.rsp-0.40.0/R.rsp/tests/rsource.R | 2 R.rsp-0.40.0/R.rsp/tests/rstring.R | 3 R.rsp-0.40.0/R.rsp/vignettes/RSP_intro.md.rsp | 8 R.rsp-0.40.0/R.rsp/vignettes/RSP_refcard.tex.rsp | 2 R.rsp-0.40.0/R.rsp/vignettes/R_packages-LaTeX_vignettes.ltx | 9 R.rsp-0.40.0/R.rsp/vignettes/R_packages-RSP_vignettes.md.rsp | 2 103 files changed, 1440 insertions(+), 1210 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Vijay Barve [ctb],
Dan Mcglinn [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.9.5 dated 2016-10-06 and 0.9.6 dated 2016-12-06
DESCRIPTION | 10 +++---- MD5 | 28 ++++++++++---------- NEWS.md | 17 ++++++++++-- R/oai-pmh.R | 50 +++++++++++++++++++------------------ R/parsenames.R | 18 ++++++++----- build/vignette.rds |binary man/gbif_oai.Rd | 48 +++++++++++++++++++---------------- man/occ_data.Rd | 6 ++-- man/occ_search.Rd | 6 ++-- man/parsenames.Rd | 13 +++++---- tests/testthat/test-name_lookup.r | 2 - tests/testthat/test-name_suggest.r | 8 ++--- tests/testthat/test-oai.R | 14 ++++++---- tests/testthat/test-occ_facet.R | 4 ++ tests/testthat/test-parsenames.r | 12 ++++---- 15 files changed, 134 insertions(+), 102 deletions(-)
Title: Matrix-Based Partial Least Squares Estimation
Description: Partial Least Squares Path Modeling
algorithm and related algorithms. The algorithm implementations aim for
computational efficiency using matrix algebra and covariance data. The
package is designed toward Monte Carlo simulations and includes functions
to perform simple Monte Carlo simulations.
Author: Mikko Rönkkö [aut, cre]
Maintainer: Mikko Rönkkö <mikko.ronkko@aalto.fi>
Diff between matrixpls versions 1.0.2 dated 2016-12-05 and 1.0.3 dated 2016-12-06
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/estimator.R | 17 ++++++++++++++--- 3 files changed, 20 insertions(+), 9 deletions(-)
Title: Manly Mixture Modeling and Model-Based Clustering
Description: The utility of this package includes finite mixture modeling and model-based clustering through Manly mixture models by Zhu and Melnykov (2016) <DOI:10.1016/j.csda.2016.01.015>. It also provides capabilities for forward and backward model selection procedures.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Michael Hutt [ctb, cph] (NM optimization in c),
Stephen Moshier [ctb, cph] (eigen calculations in c),
Rouben Rostamian [ctb, cph] (memory allocation in c)
Maintainer: Xuwen Zhu <xuwen.zhu@louisville.edu>
Diff between ManlyMix versions 0.1.3 dated 2016-04-15 and 0.1.7 dated 2016-12-06
DESCRIPTION | 14 ++++---- MD5 | 26 ++++++++-------- NAMESPACE | 4 +- NEWS | 16 +++++++++ R/other.R | 77 ++++++++++++++++++++++++++++++++++++++++++++++++ demo/00Index | 1 demo/Overlap.R |only man/Manly.EM.Rd | 2 + man/Manly.contour.Rd | 1 man/Manly.overlap.Rd |only man/Manly.sim.Rd | 6 +-- man/Manly.var.Rd | 1 man/ManlyMix-package.Rd | 18 ++++++++--- man/ais.Rd | 4 -- man/bankruptcy.Rd | 2 - 15 files changed, 141 insertions(+), 31 deletions(-)
Title: Simulation and Estimation for Branching Processes
Description: Simulation and parameter estimation of multitype Bienayme - Galton - Watson processes.
Author: Camilo Jose Torres-Jimenez <cjtorresj@unal.edu.co>
Maintainer: Camilo Jose Torres-Jimenez <cjtorresj@unal.edu.co>
Diff between Branching versions 0.9.2 dated 2016-05-22 and 0.9.4 dated 2016-12-06
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/rBGWM.cc | 24 ++++++++++++------------ 3 files changed, 18 insertions(+), 18 deletions(-)